Plot hole: When Superman becomes human for Lois, the molecule chamber nearly rips him apart, he suffers. At the end of the movie, when he tricks out of the evil 3 and turn them into humans with the same radiation, they are just looking around, wondering about the strange lights, but don't suffer at all.
Continuity mistake: When the villains are trapped in the phantom zone (filmed by Richard Donner) Zod, Non and Ursa (from left to right) are tightly pressed against a glass. When the elevator explodes and are about to be released (filmed by Richard Lester) not only are they not pressed, but neither in line, having changed positions (and looks, as already listed): Non now stands above Zod and Ursa.
Revealing mistake: At the Fortress, when the villains and Superman play the appearing/disappearing trick, there's a shot with 4 Supermen onscreen, a special effect which was achieved with stand-ins. The one in front of Zod, and especially the one next to Lois look nothing like Christopher Reeve.